However, their autistic symptoms returned shortly after the drugs were stopped.
The study, carried out at the Rush-Presbyterian-St Luke's Medical Center in Chicago, is being presented as evidence that disruption in gut bacteria was a cause of certain cases of autism.
Autism affects approximately one child in 150, develops usually before the child is two years old. It involves loss of language, social and play skills.
Only a small number of children were treated, all of whom had been found to have a particular type of bacterium colonising their guts.
Bacterial neurotoxin
These bacteria produces a toxin which scientists theorised might be affecting their brains.
The children were given an antibiotic targeted at this bacterium - nine out of the 11 treated enjoyed improved cognitive function, behaviour and social skills.
Dr Richard Sandler, director of paediatric gastroenterology at Rush Children's Hospital, who led the study, said: "Autism is a devastating disorder with essentially no meaningful treatment.
"Seeing most of these children apparently improve significantly was very exciting.
"The next step, besides repeating clinical studies, is to go to the lab and try and find out why these effects may have been observed."
Unfortunately, once the treatment stopped, the symptoms reasserted themselves.
The research was sparked by the work of a Ellen Bolte, the mother of an autistic child, who developed the condition at 19 months old following several months of broad-spectrum antibiotic treatment for excess fluid in the inner ear.
She reasoned that the initial antibiotic treatment had disrupted the natural bacteria which line the gut - called the intestinal flora.
With this "damaged", other bacteria which could produce harmful toxins could get a foothold and colonise the gut.
She said: "It was not long ago that patients diagnosed with peptic ulcers were advised to watch their diet and reduce stress.
"Now, it is well-established that most peptic ulders are caused by Helicobacter pylori - a bacteria - and can be cured by antibiotic treatment."